As you know, .htaccess files are read every time you access a directory in which they are "activated".

Putting your mod-perl related directives into a .htaccess file would really defeat the whole purpose of mod-perl which is to provide you with a persistent perl interpreter which keeps in memory the "compiled" version of your script, thus improving its performance.

If you will re-initiate the mod-perl environment every time you access one of the scripts it will run, you are likely to be much slower than by using ordinary CGI.

Just to be curious: why would you put the mod-perl directives in a .htaccess file?